Hi Folks,

I would like to create binary masks for any given structure in aseg.mgz and aparc+aseg.mgz.
I would then also like to map the masks back to native space.

I think, I should use mri_binarize followed by mri_convert as shown in the two examples below:

Example 1:
a. mri_binarize --i mri/aseg.mgz --match 10 --o deep-gm-rois/lh-thalamus.mgz
b. mri_convert -rl mri/orig/001.mgz -rt nearest deep-gm-rois/lh-thalamus.mgz deep-gm-rois/lh-thalamus.nii

Example 2:
a. mri_binarize --i mri/aparc+aseg.mgz --match 1022 --o ctx-gm-rois/lh-postcentral.mgz
b. mri_convert -rl mri/orig/001.mgz -rt nearest ctx-gm-rois/lh-postcentral.mgz ctx-gm-rois/lh-postcentral.nii

Ques 1: Is the best approach for this task ?

I noticed in the FAQ that mri_vol2vol is recommended for conversion from freesurfer space to anantomical space.

Ques 2: Is it better to use mri_vol2vol than mri_convert with the reslice option ?
Thanks
Mehul